Main
Guangchuang Yu
Professor of Bioinformatics at Southern Medical University. I have developed more than 20 R packages, including clusterProfiler, ChIPseeker, treeio and ggtree, to help biologists to explore and understand their data.
I am broadly interested in bioinformatics, metagenomics, molecular evolution, data integration and visualization.
Research Experience
Professor
School of Basic Medical Sciences
Southern Medical University
present - 2018
- Associate director of Institute of Bioinformatics
Post-doctoral Fellow
State Key Laboratory of Infectious Diseases
The University of Hong Kong
2018 - 2017
Bioinformatician
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes
Jinan University
2013 - 2009
Education
PhD., Bioinformaitcs
The University of Hong Kong
Hong Kong, CN
2017 - 2013
- Thesis: Big-data computational methods for studying molecular evolution: from accurate genome assembly to phylogenetic analysis and data integration
M.S., Biochemistry and Molecular Biology
Anhui Medical University
Hefei, CN
2009 - 2006
- Thesis: miRNA靶基因计算分析新方法及其应用研究
B.S., Biotechnology
South China Agricultural University
Guangzhou, CN
2005 - 2001
南方医科大学高层次人才“不忘初心 牢记使命”学习教育
延安干部培训学院
Yan’an, CN
2018
Train the Trainers
Institut Pasteur
Paris, FR
2015
Certificate
Certificate of Teaching and Learning in Higher Education
Centre for Enhancement of Teaching and Learning
The University of Hong Kong
2015
Teaching Experience
BMB209: Workshops in Applied Bioinformatics
Department of Biochemistry and Molecular Biology
University of Southern Denmark
2019
- PhD level class, invited lecture
生物信息学科研训练
School of Basic Medical Sciences
Southern Medical University
- Undergraduate level class
基因组学
School of Basic Medical Sciences
Southern Medical University
- Undergraduate level class
基础医学新进展讲座
School of Basic Medical Sciences
Southern Medical University
- Undergraduate level class
功能蛋白质研究
College of Life Science and Technology
Jinan University
2012 - 2011
- Graduate level class
Grants
南方医科大学第三层次人才引进科研项目 (G618289088)
PI, CNY ¥1,500,000
N/A
2020 - 2018
hnRNPK蛋白在调控人肺癌细胞周期胞质分裂中的作用研究 (21613414)
PI, CNY ¥100,000, 中央高校基本科研业务费专项资金
N/A
2013
Hela细胞周期动态蛋白质组学分析 (21611303)
PI, CNY ¥20,000, 中央高校基本科研业务费专项资金
N/A
2011
Books
生物信息学II
《功能蛋白质研究》. 385-425. 何庆瑜(主编),科学出版社 (“十二五”国家重点图书出版规划项目)
N/A
2012
- 余光创
Publications
- Citation = 3625
- H-index = 16
- I10-index = 22
Two methods for mapping and visualizing associated data on phylogeny using ggtree
Molecular Biology and Evolution. 2018, 35(12):3041-3043.
N/A
2018
- G Yu*, TTY Lam, H Zhu, Y Guan*
- Impact Factor = 14.797
Using meshes for MeSH term enrichment and semantic analyses
Bioinformatics. 2018, 34(21):3766–3767.
N/A
- G Yu
ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
Methods in Ecology and Evolution. 2017, 8(1):28-36
N/A
2017
- G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*
- ESI Highly Cited Paper
ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
Molecular BioSystems. 2016, 12(2):477-479
N/A
2016
- G Yu, QY He*
- ESI Highly Cited Paper
Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae
Frontiers in Microbiology. 2016, 7:78
N/A
- XY Yang, K He, G Du, X Wu, G Yu, Y Pan, G Zhang*, X Sun*, QY He*
Genetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015
Infection, Genetics and Evolution. 2016, 38:96-100
N/A
- PY Huang, CCD Lee, CH Yip, CL Cheung, G Yu, TTY Lam, DK Smith, H Zhu*, Y Guan*
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization
Bioinformatics. 2015, 31(14):2382-2383
N/A
2015
- G Yu*, LG Wang, QY He*
- ESI Highly Cited Paper
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
Bioinformatics. 2015, 31(4):608-609
N/A
- G Yu*, LG Wang, GR Yan, QY He*
ACK1 Promotes Gastric Cancer Epithelial-Mesenchymal Transition and Metastasis through AKT-POU2F1-ECD Signaling
Journal of Pathology. 2015, 236(2):175-185
N/A
- SH Xu, JZ Huang, ML Xu, G Yu, XF Yin, D Chen*, GR Yan*
Proteomic analysis on the copper resistance of Streptococcus pneumonia
Metallomics. 2015, 7(3):448-454
N/A
- Z Guo, J Han, XY Yang, K Cao, K He, G Du, G Zeng, L Zhang, G Yu, Z Sun, QY He*, X Sun*
Proteomic analysis on the antibacterial activity of a Ru(II) complex against Strepococcus pneumonia
Journal of Proteomics. 2015, 115:107-116
N/A
- XY Yang, L Zhang, J Liu, N Li, G Yu, K Cao, J Han, G Zeng, Y Pan, X Sun*, QY He*
Proteomic analysis of putative heme-binding proteins in Streptococcus pyogenes
Metallomics. 2014, 6(8):1451-1459
N/A
2014
- N Wang#, J Zhang#, L Zhang, XY Yang, N Li, G Yu, J Han, K Cao, Z Guo, X Sun*, QY He*
Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumonia
Metallomics. 2013, 5(7):928-935
N/A
2013
- X Sun#, G Yu#, Q Xu, N Li, C Xiao, X Yin, K Cao, J Han, QY He*
A novel andrographolide derivative AL-1 exerts its cytotoxicity on K562 cells through a ROS-dependent mechanism
Proteomics, 2013, 13(1):169-178
N/A
- YY Zhu#, G Yu#, Y Zhang, Z Xu, YQ Huang, GR Yan*, QY He*
A DNA-Based Semantic Fusion Model for Remote Sensing Data
PLoS One. 2013, 8(10):e77090
N/A
- H Sun*, J Weng, G Yu, RH Massawe
Quantitative Proteomics Characterization on the Anti-tumor Effects of Isodexyelephantopin against Nasopharyngeal Carcinoma
Proteomics. 2013, 13(21):3222-3232
N/A
- GR Yan#, Z Tan#, Y Wang, ML Xu, G Yu, Y Li*, QY He*
Design, SAR, angiogenic activities evaluation and pro-angiogenic mechanism of new marine cyclopeptide analogs
Current Medicinal Chemistry. 2013, 20(9):1183-1194
N/A
- J Li, X Lu, Q Wu, G Yu, Z Xu, L Qiu, Z Pei, Y Lin, J Pang*
Proteomic investigation of the interactome of FMNL1 in hematopoietic cells unveils a role in calcium-dependent membrane plasticity
Journal of Proteomics. 2013, 78:72-82
N/A
- Y Han, G Yu, H Sarioglu, A Caballero-Martinez, F Schlott, M Ueffing, H Haase, C Peschel, AM Krackhardt*
LXtoo: an integrated live Linux distribution for the bioinformatics community
BMC Research Notes. 2012, 5(1):360
N/A
2012
- G Yu#, LG Wang#, XH Meng, QY He*
clusterProfiler: an R package for comparing biological themes among gene clusters
OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287
N/A
- G Yu, LG Wang, Y Han, QY He*
- ESI Highly Cited Paper
Cellular MicroRNA let-7c Inhibits M1 Protein Expression of the H1N1 Influenza A Virus in Infected Human Lung Epithelial Cells
Journal of Cellular and Molecular Medicine. 2012, 16(10):2539-2546
N/A
- Y Ma#, J Yang#, X Fan#, H Zhao, W Hu, Z Li, G Yu, X Ding, J Wang, X Bo, X Zheng, Z Zhou*, S Wang*
Genistein-induced mitotic arrest of gastric cancer cells by downregulating KIF20A, a proteomics study
Proteomics. 2012, 12(14):2391-2399
N/A
- GR Yan#, FY Zhou#, BL Dang, Y Zhang, G Yu, X Liu, QY He*
Functional similarity analysis of human virus-encoded miRNAs
Journal of Clinical Bioinformatics. 2011, 1(1):15
N/A
2011
- G Yu, QY He*
A new method for measuring functional similarity of microRNAs
Journal of Integrated OMICS. 2011, 1(1):49-54
N/A
- G Yu#, CL Xiao#, X Bo, CH Lu, Y Qin, S Zhan, QY He*
Phosphoproteome profile of human lung cancer cell line A549
Molecular BioSystems. 2011, 7(2):472-479
N/A
- G Yu#, CL Xiao#, CH Lu#, HT Jia, F Ge, W Wang, XF Yin, HL Jia, JX He*, QY He*
Proteomic Analysis of Membrane Proteins from Streptococcus pneumoniae with Multiple Separation Methods plus High Accuracy Mass Spectrometry
OMICS: A Journal of Integrative Biology. 2011, 15(10):683-694
N/A
- X Sun#, XY Yang#, XF Yin, G Yu, CL Xiao, X He, QY He*
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
Bioinformatics. 2010, 26(7):976-978
N/A
2010
- G Yu#, F Li#, Y Qin, X Bo*, Y Wu, S Wang*
- ESI Highly Cited Paper
结合基因组分析预测炎症相关miRNA及其靶标
军事医学科学院院刊. 2009, 33(3):245-247
N/A
2009
- 余光创,王超,许尹,伯晓晨,王升启*,秦宜德*
依赖于5’端非编码区高级结构的真核生物mRNA翻译调控
中国生物化学与分子生物学报. 2007, 23(11):881-887
N/A
2007
- 余光创,秦宜德,伯晓晨,王升启*
Conference proceedings
Two methods for mapping and visualizing associated data on phylogeny using ggtree
第一届南方医科大学基础医学学术年会
Guangzhou, CN
2019
Data integration and visualization of phylogenetic trees
The 3rd South Lake Innovation Forum for International Young Talents
Wuhan, CN
2018
ggtree for tree visualization & annotation
Phylogenetic tree visualization workshop/hackathon
Chicago, US
2017
Computational Methods in Ecology and Evolution
The Second International Workshop on Environmental Microbiomes
Guangzhou, CN
ggtree for visualization and annotation of phylogenetic trees
The 9th China-R Conference
Beijing, CN
2016